[2023-06-30 20:38:01,272] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:38:01,275] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:38:01,276] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference
[2023-06-30 20:38:03,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:38:03,460] [INFO] Task started: Prodigal
[2023-06-30 20:38:03,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f9e4a3d-fb41-42ec-9aef-ed71b3dd8bd3/GCA_025057075.1_ASM2505707v1_genomic.fna.gz | prodigal -d GCA_025057075.1_ASM2505707v1_genomic.fna/cds.fna -a GCA_025057075.1_ASM2505707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:38:07,703] [INFO] Task succeeded: Prodigal
[2023-06-30 20:38:07,704] [INFO] Task started: HMMsearch
[2023-06-30 20:38:07,704] [INFO] Running command: hmmsearch --tblout GCA_025057075.1_ASM2505707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference/reference_markers.hmm GCA_025057075.1_ASM2505707v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:38:07,887] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:38:07,889] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6f9e4a3d-fb41-42ec-9aef-ed71b3dd8bd3/GCA_025057075.1_ASM2505707v1_genomic.fna.gz]
[2023-06-30 20:38:07,912] [INFO] Query marker FASTA was written to GCA_025057075.1_ASM2505707v1_genomic.fna/markers.fasta
[2023-06-30 20:38:07,912] [INFO] Task started: Blastn
[2023-06-30 20:38:07,912] [INFO] Running command: blastn -query GCA_025057075.1_ASM2505707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference/reference_markers.fasta -out GCA_025057075.1_ASM2505707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:38:08,470] [INFO] Task succeeded: Blastn
[2023-06-30 20:38:08,493] [INFO] Selected 7 target genomes.
[2023-06-30 20:38:08,494] [INFO] Target genome list was writen to GCA_025057075.1_ASM2505707v1_genomic.fna/target_genomes.txt
[2023-06-30 20:38:08,496] [INFO] Task started: fastANI
[2023-06-30 20:38:08,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f9e4a3d-fb41-42ec-9aef-ed71b3dd8bd3/GCA_025057075.1_ASM2505707v1_genomic.fna.gz --refList GCA_025057075.1_ASM2505707v1_genomic.fna/target_genomes.txt --output GCA_025057075.1_ASM2505707v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:38:11,521] [INFO] Task succeeded: fastANI
[2023-06-30 20:38:11,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:38:11,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:38:11,524] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:38:11,525] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:38:11,525] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-30 20:38:11,527] [INFO] DFAST Taxonomy check result was written to GCA_025057075.1_ASM2505707v1_genomic.fna/tc_result.tsv
[2023-06-30 20:38:11,528] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:38:11,528] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:38:11,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference/checkm_data
[2023-06-30 20:38:11,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:38:11,560] [INFO] Task started: CheckM
[2023-06-30 20:38:11,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025057075.1_ASM2505707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025057075.1_ASM2505707v1_genomic.fna/checkm_input GCA_025057075.1_ASM2505707v1_genomic.fna/checkm_result
[2023-06-30 20:38:31,508] [INFO] Task succeeded: CheckM
[2023-06-30 20:38:31,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.96%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:38:31,535] [INFO] ===== Completeness check finished =====
[2023-06-30 20:38:31,536] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:38:31,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025057075.1_ASM2505707v1_genomic.fna/markers.fasta)
[2023-06-30 20:38:31,537] [INFO] Task started: Blastn
[2023-06-30 20:38:31,537] [INFO] Running command: blastn -query GCA_025057075.1_ASM2505707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d45141-3293-4ea8-bb77-26a23379d1b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_025057075.1_ASM2505707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:38:32,257] [INFO] Task succeeded: Blastn
[2023-06-30 20:38:32,262] [INFO] Selected 9 target genomes.
[2023-06-30 20:38:32,262] [INFO] Target genome list was writen to GCA_025057075.1_ASM2505707v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:38:32,270] [INFO] Task started: fastANI
[2023-06-30 20:38:32,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f9e4a3d-fb41-42ec-9aef-ed71b3dd8bd3/GCA_025057075.1_ASM2505707v1_genomic.fna.gz --refList GCA_025057075.1_ASM2505707v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025057075.1_ASM2505707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:38:36,461] [INFO] Task succeeded: fastANI
[2023-06-30 20:38:36,465] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:38:36,466] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001458695.1	s__Nitrospira_F inopinata	79.6687	154	259	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:38:36,468] [INFO] GTDB search result was written to GCA_025057075.1_ASM2505707v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:38:36,469] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:38:36,471] [INFO] DFAST_QC result json was written to GCA_025057075.1_ASM2505707v1_genomic.fna/dqc_result.json
[2023-06-30 20:38:36,471] [INFO] DFAST_QC completed!
[2023-06-30 20:38:36,471] [INFO] Total running time: 0h0m35s